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Genome Studies for Drug Safety

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Ernie Bush, VP and Scientific Director, Cambridge Healthtech Associates : The following is an interview that Ernie Bush conducted with Paul Watkins in September 2010.     

Paul Watkins, Professor of Medicine and Pharmacy at the University of North Carolina, Chapel Hill, and director of the Hamner-UNC Institute for Drug Safety Sciences, spoke with me about the Hamner Institute’s efforts to leverage information from the human genome to explore issues around drug induced liver injury.

EB: Could you describe the work you’re doing at the Hamner Institute?

PW: Rare idiosyncratic drug induced liver injury (DILI) is the major drug toxicity that terminates a new molecular entity in clinical development and it’s also the major organ toxicity that leads to regulatory actions on drugs post approval. And there’s really been very little insight to date on what is the mechanism of these adverse events, i.e. why a drug that’s safe for the vast majority of people can cause life threatening liver injury in a rare person, say 1 in 10,000 or 1 in 50,000. And a very exciting endeavor that’s been ongoing now for five years and funded by the NIH is the drug induced liver injury network or DILIN.

I chair the steering committee and I also chair the genetics sub-committee for this initiative. It involves finding people around the country who’ve actually had these rare reactions and recovered, in some cases after a liver transplant. And one of the first areas we’re starting on is the genetics. All of these subjects are going to undergo the million SNP chip analysis for a genome-wide association study (GWAS). About half of the 850 have already had this GWAS and there have been some successes just doing this technique.

To extend this assessment, what we’re now embarking on, and this is in collaboration with David Goldstein’s group at Duke, is whole exome sequencing with cases due to certain drugs where we have a relatively large number of well-characterized subjects... There’s also a parallel effort in Europe...

All these studies in the U.S. and Europe are, of course, generating a huge amount of data. Therefore, the real challenge now is: How do we mine that large data set to get mechanistic insight of why an individual would be susceptible to DILI drug reactions. So here at the Hamner, we’ve begun several research initiatives designed to synergize and capitalize on these other resources.

One is that we’re looking at panels of inbred mice that are genetically very well characterized but one strain is significantly different from the other. We use these strains as a model for genetic variation that exists in people. We were fortunate enough to get an NIH grant—that’s myself and David Threadgill who’s the chair of genetics at NC State University—to start giving drugs to these mice to see if we could find one particular strain or a couple of strains that would manifest the toxicity, just as it occurs in people. Because the genetics is very well worked out and established in these mice, we can immediately see candidate genes that account for the susceptibility in mice and then compare that to the human genetic data in the DILIN and SAE consortium gene banks to test these hypotheses.

The other approach is to study the effects of these drugs, the ones implicated as causing liver injury, in primary cultures of human hepatocytes with additional cells that are present in the liver; particularly Kupffer cells to see if we can define the pathways that these drugs perturb as you go from physiologic concentrations to toxic concentrations. These studies may generate a list of suspect genes that we can then go over to the human genetic data and actually look very closely at these genes to see if there’s any variation that might cause a susceptibility to DILI.

Likewise as David Goldstein’s group comes up with certain genetic variations that they say statistically are different between the cases and controls, we can go to our hepatocytes and look to see if that makes sense mechanistically.

And then lastly, we’re putting all this information together in an in silco model called DILI-SIM. This work is a collaboration between the Food and Drug Administration and a Bay area company called Entelos where we’ve already begun modeling the major pathways taken by drugs and the major perturbations that drugs cause that can lead to liver toxicity.

EB: At the World Pharmaceutical Congress, you presented preliminary data that suggest not so much a metabolic difference in these individuals, but an immune system difference, is that correct?

PW: That’s right. One of the surprises in the GWAS analysis, both done in the DILIN and the SAE consortium, was that for some drugs the major susceptibility factor that we could identify was within what’s called the HLA region of the genome. So this is involved in the immune response—what’s called the acquired immune response, suggesting that these severe events may in some cases be due to the body’s immune system attacking the liver.

In addition to that, we found suggestions for other types of genes including drug metabolism and transporter genes. But, the associations so far have been weak and we’ve actively working to improve and expand these findings.

This article also appeared in the September-October 2010 issue of Bio-IT World 

I-Study: Genomic Interpretation - Who Will Pay?
During this webinar, members of the study review team present preliminary findings of the I-Study, conducted at the Harvard Medical School's 2011 Personalized Medicine Conference.
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